CoxBase: an online platform for epidemiological surveillance, visualization, analysis and typing of Coxiella burnetii genomic sequences

Abstract

ABSTRACTQ (query) fever is an infectious zoonotic disease caused by the Gram-negative bacteria Coxiella burnetii. Although the disease has been studied since decades, it still represents a threat due to sporadic outbreaks across farms in Europe. The absence of a central platform for Coxiella typing data management in an important epidemiological gap which is relevant in the case of an outbreak. To fill this gap, we have designed and implemented an online, open-source, and, web-based platform called CoxBase (https://coxbase.q-gaps.de). This platform includes a database that holds genotyping information of more than 400 Coxiella isolates alongside metadata that annotates them. We have also implemented features for in silico genotyping of completely or minimally assembled Coxiella sequences using five different typing methods, querying existing isolates, visualization of isolate’s geodata via aggregation on a world map and submission of new isolates. We tested our in silico typing method on 50 Coxiella genomes downloaded from the RefSeq database and we successfully genotyped all except for cases where the sequence quality was poor. We identified new spacer sequences using our implementation of the MST in silico typing method, and established adaA gene phenotypes for all 50 genomes as well as their plasmid types.